"We back the position of the Spanish government that has to be adopted by all sides," Merkel said as she arrived for an EU leaders summit in Brussels.
"We hope there are solutions found on the basis of the Spanish constitution."
French president Emmanuel Macron commented that EU leaders will use the summit to send a "message of unity" with Madrid, meanwhile.
"This European Council will be marked by a message of unity -- unity with our member states facing crises, unity with Spain and very strong unity in discussions about Brexit," he said.
Rajoy waved to waiting journalists but remained silent as he arrived at the summit building, where he was greeted with a bear hug by European Commission President Jean-Claude Juncker.
Luxembourg's Prime Minister Xavier Bettel reiterated the oft-rehearsed European line that the crisis in Calatonia was an internal matter for Madrid.
"The Catalan problem is above all a Spanish problem, it must be resolved in Spain." he said.
One European leader who does not appear to be on the same page as Rajoy however is Belgian PM Charles Michel. The 41-year-old, who told newspaper Le Soir last weekend that the situation in Spain "relates to fundamental issues including the right to vote, opinions and the use of force," once again criticised the force used on October 1st, after arriving in Brussels.
"I continue to condemn all forms of violence and ask for dialogue. I don't think political escalation is a good thing," El Pais quotes him as saying on Thursday.
According to reports in the Belgian media, Michel's stance has caused diplomatic tension between Brussels and Madrid. Newspapers Het Laatste Nieuws and De Morgen claim that Rajoy's chief of staff told Belgium's ambassador to Spain via e-mail that the Spanish government is "stupified" by Michel's comments and they "could put our bilateral relations at serious risk".